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parsnp

https://gitlab.com/advaitb/parsnp

Science Score: 18.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (6.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: gitlab.com
  • Owner: advaitb
  • Default Branch: master
Statistics
  • Stars: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 6 years ago
Metadata Files
Readme License Citation

README.md

Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees; both Parsnp and Gingr form part of the Harvest suite :

Parsnp is primarily distributed as a binary for Linux or OS X (see Parsnp link above ). However, the source and build scripts are provided for incompatible platforms or for development purposes.

CITATION provides details on how to cite Parsnp.

INSTALL provides instructions for building from source and installing.

LICENSE provides licensing information.

Citation (CITATION) 

[Parsnp]

   Treangen TJ*, Ondov BD*, Koren S, Phillippy AM:
     Rapid Core-Genome Alignment and Visualization for Thousands of Microbial Genomes.
     bioRxiv (2014). doi: http://dx.doi.org/10.1101/007351

* These authors contributed equally to this work

External software (please also cite if you find Parsnp useful):

   [FastTree2]
   
      Price MN, Dehal PS, Arkin AP: 
        FastTree 2--approximately maximum-likelihood trees for large alignments. 
        PLoS One 2010, 5:e9490.
   
   [Muscle]
   
      Edgar RC:
        MUSCLE: multiple sequence alignment with high accuracy and high throughput. 
        Nucleic Acids Research 2004, 32:1792-1797.
   
   [PhiPack]

      Bruen TC, Philippe H, Bryant D: 
        A simple and robust statistical test for detecting the presence of recombination. 
        Genetics 2006, 172:2665-2681.